Molecular Docking, Topological Analysis and Vibrational Studies on N-(2-Bromoethyl) Succinimide: Antidepressant Agent

2020 ◽  
Vol 17 ◽  
Author(s):  
Aslı Eşme
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Topological Analysis ◽  
Biological Properties ◽  
Vibrational Frequencies ◽  
Oscillator Strengths ◽  
Potential Energy Distribution ◽  
Geometrical Parameters ◽  
Molecular Docking Study ◽  
Excitation Energies

Abstract:: N-(2-Bromoethyl) succinimide (N2BES) is a compound with antidepressant pharmacological properties. N-(2-Bromoethyl) succinimide was analyzed for its structural, electronic, vibrational, topological, and biological properties. The molecular geometrical parameters such as bond lengths (Å), bond angles (º), and dihedral angles (º) of N2BES and harmonic vibrational frequencies were investigated using the density functional theory calculations with the B3LYP/6-311++G(d,p) level of theory. Experimental vibrational frequencies of N2BES were recorded in the region 4000–400 cm-1 (FT-IR) and 4000–100 cm-1 (FT-Raman) and compared with the theoretical frequencies were made on the basis of potential energy distribution (PED) analysis. Frontier molecular orbitals (FMOs), global reactivity descriptors, density of states (DOS) prop-erties, molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis, topological analysis of the reduced density gradient (RDG), localized orbital locator (LOL), bond critical points (BCP) for N2BES are investigated by theoret-ical calculations. The experimental UV-Vis measured within the 200-500 nm and calculated electronic transitions of ab-sorption wavelength (λ), excitation energies (E), oscillator strengths (f), and assignments in ethanol solvent. In addition, the molecular docking study of the title molecule predicts its binding orientation in the active site of the target serotonin 1A (5-HT1A) protein.

scholarly journals Molecular structure, vibrational spectra, NBO, Fukui function, HOMO-LUMO analysis and molecular docking study of 6-[(2-methylphenyl)sulfanyl]-5-propylpyrimidine-2,4(1H,3H)-dione

2017 ◽  
Vol 36 (1) ◽  
Author(s):  
Haitham AlRabiah ◽  
S Muthu ◽  
Fatmah Al-Omary ◽  
Abdul-Malek Al-Tamimi ◽  
M Raja ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Electron Density ◽  
Density Of States ◽  
Title Compound ◽  
Density Functional ◽  
Basis Set ◽  
Geometrical Parameters ◽  
Total Density ◽  
Molecular Docking Study ◽  
Homo Lumo

Theoretical and experimental FT-IR and FT-Raman vibrational spectral analysis of 6-[(2-methylphenyl)sulfanyl]-5-propylpyrimidine-2,4(1H,3H)-dione have been recorded in the region 4000-400 cm-1 and 4000-100 cm-1 insolid phase. The molecular geometrical parameters, bond length, bond angle and vibrational wave numbers, harmonic vibrational frequency were investigated using the density functional theory B3LYP method with the 6-311++G(d,p) basis set. The stability of the molecule has been investigated using the natural bond orbital (NBO) analysis. The electronic properties such as HOMO-LUMO energies were determined by the time-dependent DFT approach. The thermodynamical properties and the first order hyperpolarizability and molecular electrostatic potential (MEP) of the title compound were also studied. The electron density-based local reactivity descriptors such as the Fukui functions were calculated to explain the chemical selectivity or reactivity site in the molecule. The molecule orbital contributions were investigated using the total density of states (TDOS), the sum of 𝛼 and 𝛽 electron density of states (𝛼𝛽DOS). The molecular docking (ligand-protein) simulations have been performed using the SWISSDOCK server. The full fitness (FF) score and hydrogen bonding interaction and binding affinity values revealed that title compound can act as potential inhibitor against HIV-1 protease.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

scholarly journals Design, Synthesis, and Molecular Docking Study of New Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors Combining Resin Acids and Adamantane Moieties

2021 ◽  
Vol 14 (5) ◽  
pp. 422
Author(s):  
Kseniya Kovaleva ◽  
Olga Yarovaya ◽  
Konstantin Ponomarev ◽  
Sergey Cheresiz ◽  
Amirhossein Azimirad ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Biological Properties ◽  
Glioma Cell Line ◽  
Resin Acids ◽  
Adamantane Derivatives ◽  
Molecular Docking Study ◽  
Design Synthesis ◽  
Low Cytotoxicity ◽  
Covalent Intermediate

In this paper, a series of novel abietyl and dehydroabietyl ureas, thioureas, amides, and thioamides bearing adamantane moieties were designed, synthesized, and evaluated for their inhibitory activities against tyrosil-DNA-phosphodiesterase 1 (TDP1). The synthesized compounds were able to inhibit TDP1 at micromolar concentrations (0.19–2.3 µM) and demonstrated low cytotoxicity in the T98G glioma cell line. The effect of the terpene fragment, the linker structure, and the adamantane residue on the biological properties of the new compounds was investigated. Based on molecular docking results, we suppose that adamantane derivatives of resin acids bind to the TDP1 covalent intermediate, forming a hydrogen bond with Ser463 and hydrophobic contacts with the Phe259 and Trp590 residues and the oligonucleotide fragment of the substrate.

scholarly journals The Effect of Geometrical Isomerism of 3,5-Dicaffeoylquinic Acid on Its Binding Affinity to HIV-Integrase Enzyme: A Molecular Docking Study

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Mpho M. Makola ◽  
Ian A. Dubery ◽  
Gerrit Koorsen ◽  
Paul A. Steenkamp ◽  
Mwadham M. Kabanda ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Catalytic Domain ◽  
Synergistic Activity ◽  
Hiv Integrase ◽  
Molecular Docking Study ◽  
Geometrical Isomers ◽  
Catalytic Core ◽  
Dicaffeoylquinic Acid ◽  
Hiv 1

A potent plant-derived HIV-1 inhibitor, 3,5-dicaffeoylquinic acid (diCQA), has been shown to undergo isomerisation upon UV exposure where the naturally occurring3trans,5trans-diCQA isomer gives rise to the3cis,5trans-diCQA,3trans,5cis-diCQA, and3cis,5cis-diCQA isomers. In this study, inhibition of HIV-1 INT by UV-induced isomers was investigated using molecular docking methods. Here, density functional theory (DFT) models were used for geometry optimization of the 3,5-diCQA isomers. The YASARA and Autodock VINA software packages were then used to determine the binding interactions between the HIV-1 INT catalytic domain and the 3,5-diCQA isomers and the Discovery Studio suite was used to visualise the interactions between the isomers and the protein. The geometrical isomers of 3,5-diCQA were all found to bind to the catalytic core domain of the INT enzyme. Moreover, thecisgeometrical isomers were found to interact with the metal cofactor of HIV-1INT, a phenomenon which has been linked to antiviral potency. Furthermore, the3trans,5cis-diCQA isomer was also found to interact with both LYS156 and LYS159 which are important residues for viral DNA integration. The differences in binding modes of these naturally coexisting isomers may allow wider synergistic activity which may be beneficial in comparison to the activities of each individual isomer.

scholarly journals Molecular Structure, vibrational spectra, Molecular Docking and ADMET Study of Cellulose Triacetate II-=SUP=-*-=/SUP=-

2020 ◽  
Vol 128 (8) ◽  
pp. 1128
Author(s):  
Sefa Celik ◽  
A. Demet Demirag ◽  
Aysen E. Ozel ◽  
Sevim Akyuz
Keyword(s):  
Molecular Structure ◽  
Molecular Docking ◽  
Aspergillus Niger ◽  
Density Functional ◽  
Cellulose Triacetate ◽  
Potential Energy Distribution ◽  
Cellulase Enzyme ◽  
Important Relationship ◽  
In Silico Admet ◽  
Nano Cluster

People have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental problems that remain intact in nature for years. In this study, molecular structure analysis of cellulose triacetate II (CTA II) molecule, obtained from cellulose II and acetate, was carried out. There is an important relationship between the structure and activity of molecules, so it is very important to determine the geometric structure of a molecule. Therefore, using density functional theory (DFT) the most stable molecular geometries of the cellulose triacetate II monomer (C12H18O9) as well as dimer (C24H36O18), which included intermolecular H-bonding, were calculated. The analogous calculations were carried out for the (CTA-II)2 nano-cluster (C24H34O17), which represents the local structure of CTA-II crystal, and created by binding the two most stable CTA II molecules by covalent bond. Scaled wavenumbers and potential energy distribution of the vibrational modes of CTA monomer and (CTA-II)2 nano-cluster were computed. In order to evaluate the interaction of CTA II with the Aspergillus niger cellulase enzyme,which is an important that is active in cellulose digestion and CTA II, molecular docking studies were carried out. H-binding interactions between CTA II (in monomeric, dimeric and cluster forms) and the active site of the Aspergillus niger cellulase enzyme were shown. Moreover, in silico ADMET prediction study was calculated for CTA-II monomer to predict its druglikeness properties. Keywords: Cellulose triacetate II, Density Function Theory, IR-ATR, cluster for.

scholarly journals Unraveling the Effects of Co-Crystallization on the UV/Vis Absorption Spectra of an N-Salicylideneaniline Derivative. A Computational RI-CC2 Investigation

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4512
Author(s):  
Jean Quertinmont ◽  
Tom Leyssens ◽  
Johan Wouters ◽  
Benoît Champagne
Keyword(s):  
Optical Properties ◽  
Crystal Field ◽  
Indirect Effects ◽  
Density Functional ◽  
Crystal Packing ◽  
Density Functional Theory Method ◽  
Oscillator Strengths ◽  
Excitation Energies ◽  
Keto Form ◽  
Cell Parameters

This work aims at unraveling the effects of co-crystallization on the optical properties of an N-salicylideneaniline-derived molecular switch transforming between an enol and a keto form. This is achieved by way of a two-step multi-scale method where (i) the molecular geometry and unit cell parameters are optimized using a periodic boundary conditions density functional theory method and (ii) the optical properties are computed for a selection of clusters embedded in an array of point-charges that reproduce the crystal field electronic potential. The optical properties (vertical excitation energies and oscillator strengths) are obtained at the RI-CC2/def2-TZVPD level of approximation. This method allows us to decompose the effects of co-crystallization into (i) indirect effects, the geometry changes of the chromophore due to crystal packing with the coformer, and (ii) direct ones, the polarization due to the interacting coformer and to the crystal field. For the former effects, variations of a crucial torsion angle lead to modification of the π-conjugation and therefore to the decrease or increase of the excitation energies. About the latter, they are antagonistic: (i) the coformer is not directly involved in the excitations but its polarization decreases the excitation energies while (ii) the crystal field has the opposite effect. For the co-crystals with succinic and fumaric acids, combining these direct and indirect effects leads to a hypsochromic shift of the first absorption band with respect to the reference crystal, in agreement with experimental data.

scholarly journals Molecular docking study of the phytol and its derivatives against COX-2 induced inflammation: A combined density functional study

2020 ◽  
pp. 1-5
Author(s):  
Muhammad Torequl Islam ◽  
Pranta Ray ◽  
Abul Bashar Ripon Khalipha ◽  
SM Hafiz Hassan ◽  
Md. Roich Khan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Docking Study ◽  
Functional Study ◽  
Molecular Docking Study ◽  
Study Results ◽  
Homo And Lumo ◽  
Cox 2

This study aimed to determine the activity of PYT and its derivatives against COX-2, including 5IKR protein induced inflammation by using the computational tools. PYT and its derivatives have been designed by utilizing density functional theory (DFT) and the performance of the drugs was also evaluated by molecular docking study. Results suggest that the NH2 derivative of PYT (D-NH2) showed binding energy -6.4 (Kcal/mol) with protein 5IKR of COX-2 compared to the main drug (D) that showed binding energy -5.1 (Kcal/mol) with the same protein. HOMO and LUMO energy values were also calculated to determine the chemical reactivity of all the modified drugs. Non-covalent interactions of PYT and its derivatives were essential in improving the performance. In conclusion, D-NH2 showed better preference in inhibiting to the protein 5IKR of COX-2 compared to other modified drugs and it can be claimed that D-NH2 will be the best conformer for COX-2 induced inflammation.

scholarly journals DFT and Molecular Docking Study of 2-[2-(4-Chlorophenylaminothiazol-5-yl]benzothiazole

2019 ◽  
Vol 31 (3) ◽  
pp. 695-698
Author(s):  
N.S. Femila Nirmal ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Docking ◽  
Atomic Charge ◽  
Molecular Geometry ◽  
Docking Study ◽  
Vibrational Frequencies ◽  
Molecular Docking Study ◽  
B3lyp Method ◽  
Homo And Lumo ◽  
Charge Analysis ◽  
Vibrational Bands

The title compound was computed by means of DFT chemical quantum calculations to obtain optimized molecular geometry, harmonic vibrational frequencies and atomic charges. Vibrational bands to the various structural groups and their importance were predicted by analyzing the vibrational spectra. The data showed that B3LYP method provide satisfactory data for assigning vibrational frequencies and structural properties.The HOMO and LUMO energies calculated permit the determination of atomic and molecular parameters and they also represented the transfer of charge in the molecule. Mulliken atomic charge analysis was also done. A comprehensive molecular picture of 2-[2-(4-chlorophenylaminothiazol-5-yl]benzothiazole and its interactions were got from NBO investigations. The molecular docking study indicates that benzothiazole derivative may possess inhibitory activity against BCL2 pancreatic cancer cell lines.

Geometry Optimization, UV/Vis, NBO, HOMO and LUMO, Excited State and Antioxidant Evaluation of Pyrimidine Derivatives

2020 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Evgeni Kvasyuk ◽  
Aliaksei G. Sysa ◽  
Radwan Alnajjar ◽  
...  
Keyword(s):  
Density Functional ◽  
Antioxidant Properties ◽  
Geometry Optimization ◽  
Dft Method ◽  
Oscillator Strengths ◽  
Equilibrium Geometry ◽  
Pyrimidine Derivatives ◽  
Excitation Energies ◽  
Solvent Water ◽  
Homo And Lumo

: In this research, the four pyrimidine derivatives have been studied by using density functional theory (DFT/B3LYP/6-31G*) in solvent water for the first time. After quantum-chemical calculations, the title compounds have been synthesized. The electronic spectra of the new derivatives in a solvent water were performed by time-dependent DFT (TD-DFT) method. The equilibrium geometry, the HOMO and LUMO orbitals, MEP, excitation energies, natural charges, oscillator strengths for the molecules have also been calculated. NBO analysis has been calculated in order to elucidate the intramolecular, rehybridization and delocalization of electron density. These molecules have high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds. Antioxidant properties of the title compounds have been investigated and discussed.

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